Not everyone that tried to by an iPhone 3G at an AT&T store on Friday was able to get their hands on one, so the cell carrier has begun letting customers pre-order their combination iPod and smartphone for in-store pick up. At least some eastern U.S. AT&T locations started offering to pre-order, or essentially reserve, an iPhone for customers after their inventories were depleted.

AT&T stores in Manchester, Maryland, and Newington, Connecticut, both confirmed that customers could reserve an iPhone 3G from future shipments. Some iPhone hopefuls will be able to pick up their new handheld as early as Saturday while others could be left waiting for days.

The move to let customers pre-order an iPhone 3G could make some shoppers happy in the short term, but if AT&T stores aren’t able to replenish their stock quick enough, it could leave other customers unhappy when they find that phones seem unavailable for days on end.

In sharp contrast, many Apple retail stores have more than enough iPhones on hand to meet customer demand. Unfortunately, the company had issues most of the day simply selling iPhones thanks to overloaded AT&T servers. Of the customers that could purchase an iPhone, most left the store with non-functioning units since AT&T’s activation servers were down as well.

So far Apple’s retail stores aren’t offering a pre-order option, and considering the number of iPhones at many Apple locations, the company likely won’t start offering the option.

Like the original iPhone launch from a year ago, Friday’s iPhone 3G launch was plagued with frustrating delays for many potential buyers. Hopefully Apple and AT&T will work out the issues before the weekend wraps up.